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- PDB-7ms0: Crystal structure of native Cg10062 -

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Basic information

Entry
Database: PDB / ID: 7ms0
TitleCrystal structure of native Cg10062
Components4-oxalocrotonate tautomerase
KeywordsHYDROLASE / tautomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / 4-oxalocrotonate tautomerase
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsNayebi, G.H. / Geiger, J.H. / Draths, K.
CitationJournal: Biochemistry / Year: 2021
Title: Cg10062 Catalysis Forges a Link between Acetylenecarboxylic Acid and Bacterial Metabolism.
Authors: Mathes Hewage, A. / Nayebi Gavgani, H. / Chi, D. / Qiu, B. / Geiger, J.H. / Draths, K.
History
DepositionMay 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-oxalocrotonate tautomerase


Theoretical massNumber of molelcules
Total (without water)19,0381
Polymers19,0381
Non-polymers00
Water1,67593
1
A: 4-oxalocrotonate tautomerase

A: 4-oxalocrotonate tautomerase

A: 4-oxalocrotonate tautomerase


Theoretical massNumber of molelcules
Total (without water)57,1153
Polymers57,1153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7400 Å2
ΔGint-39 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.577, 49.577, 80.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

21A-287-

HOH

31A-290-

HOH

41A-292-

HOH

51A-293-

HOH

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Components

#1: Protein 4-oxalocrotonate tautomerase / Cis-3-chloroacrylic acid dehalogenase


Mass: 19038.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria)
Gene: APT58_00490, AUO95_07180, CS176_0056, FM102_14895, KaCgl_17770, KbCgl_30240
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S2T163
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.55 Å3/Da / Density % sol: 17.56 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM magnesium chloride hexahydrate, 25 mM HEPES sodium, pH 7.5, 7.5% v/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→40.03 Å / Num. obs: 24562 / % possible obs: 99.94 % / Redundancy: 20 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.013 / Rrim(I) all: 0.061 / Net I/σ(I): 40.1
Reflection shellResolution: 1.37→1.42 Å / Rmerge(I) obs: 0.814 / Num. unique obs: 2401 / CC1/2: 0.911 / Rpim(I) all: 0.19 / Rrim(I) all: 0.836 / % possible all: 99.42

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3N4G

3n4g


Resolution: 1.37→40.03 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 --
Rwork0.1711 --
obs-24558 99.92 %
Displacement parametersBiso mean: 21.46 Å2
Refinement stepCycle: LAST / Resolution: 1.37→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 0 93 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481152
X-RAY DIFFRACTIONf_angle_d0.79081591
X-RAY DIFFRACTIONf_chiral_restr0.0858178
X-RAY DIFFRACTIONf_plane_restr0.0046212
X-RAY DIFFRACTIONf_dihedral_angle_d24.1283448

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